HEADER LYASE 05-JUN-07 2Q71 TITLE UROPORPHYRINOGEN DECARBOXYLASE G168R SINGLE MUTANT ENZYME IN COMPLEX TITLE 2 WITH COPROPORPHYRINOGEN-III COMPND MOL_ID: 1; COMPND 2 MOLECULE: UROPORPHYRINOGEN DECARBOXYLASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: URO-D, UPD; COMPND 5 EC: 4.1.1.37; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: UROD; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21DE3-PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-16B KEYWDS UROPORPHYRINOGEN DECARBOXYLASE ENZYME UROD G168R COPROPORPHYRINOGEN- KEYWDS 2 III PRODUCT COMPLEX, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR J.D.PHILLIPS,F.G.WHITBY,B.M.STADTMUELLER,C.Q.EDWARDS,C.P.HILL, AUTHOR 2 J.P.KUSHNER REVDAT 6 30-AUG-23 2Q71 1 REMARK REVDAT 5 20-OCT-21 2Q71 1 REMARK SEQADV REVDAT 4 18-OCT-17 2Q71 1 REMARK REVDAT 3 12-MAR-14 2Q71 1 HETNAM REVDAT 2 24-FEB-09 2Q71 1 VERSN REVDAT 1 19-JUN-07 2Q71 0 JRNL AUTH J.D.PHILLIPS,F.G.WHITBY,B.M.STADTMUELLER,C.Q.EDWARDS, JRNL AUTH 2 C.P.HILL,J.P.KUSHNER JRNL TITL TWO NOVEL UROPOPHYRINOGEN DECARBOXYLASE (URO-D) MUTATIONS JRNL TITL 2 CAUSING HEPATOERYTHROPOIETIC PORPHYRIA (HEP) JRNL REF TRANSL.RES. V. 149 85 2007 JRNL REFN ISSN 1931-5244 JRNL PMID 17240319 JRNL DOI 10.1016/J.TRSL.2006.08.006 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.5 REMARK 3 NUMBER OF REFLECTIONS : 32682 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.164 REMARK 3 R VALUE (WORKING SET) : 0.162 REMARK 3 FREE R VALUE : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.500 REMARK 3 FREE R VALUE TEST SET COUNT : 1135 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1957 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 80.15 REMARK 3 BIN R VALUE (WORKING SET) : 0.2440 REMARK 3 BIN FREE R VALUE SET COUNT : 70 REMARK 3 BIN FREE R VALUE : 0.3700 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2806 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 48 REMARK 3 SOLVENT ATOMS : 383 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.51000 REMARK 3 B22 (A**2) : -1.51000 REMARK 3 B33 (A**2) : 2.27000 REMARK 3 B12 (A**2) : -0.76000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.140 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.129 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.087 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.943 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.963 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.951 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3144 ; 0.014 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4305 ; 1.410 ; 1.962 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 395 ; 5.736 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 149 ;36.321 ;22.752 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 508 ;13.701 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 31 ;17.004 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 448 ; 0.098 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2526 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1732 ; 0.203 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2148 ; 0.306 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 327 ; 0.173 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 68 ; 0.198 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 36 ; 0.224 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1960 ; 0.904 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3087 ; 1.476 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1343 ; 2.245 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1218 ; 3.625 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. THE CRYSTALS WERE ISOMORPHOUS TO 1RY3. REMARK 4 REMARK 4 2Q71 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-JUN-07. REMARK 100 THE DEPOSITION ID IS D_1000043229. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-SEP-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : YALE FOCUSING MIRRORS, 1.5418 REMARK 200 ANGSTROM WAVELENGTH, 67 DEGREES REMARK 200 OF 0.5 DEGREE OSCILLATIONS (134 REMARK 200 IMAGES, 0-67 DEGREES) PLUS 12 REMARK 200 DEGREES OF 0.25 DEGREE REMARK 200 OSCILLATIONS (48 IMAGES 65-77 REMARK 200 DEGREES) REMARK 200 OPTICS : YALE FOCUSING MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32683 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.5 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.07800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 82.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.44200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: 1RY3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.76 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTIEN AT 6.5 MG/ML IN 50MM TRIS, PH REMARK 280 7.5, 1MM BME WAS MIXED 5 PARTS TO 3 PARTS OF PRECIPITANT (1.7M REMARK 280 CITRATE, PH 7.0) AND EQUILIBRATED BY SITTING DROP VAPOR REMARK 280 DIFFUSION AGAINST A WELL OF PRECIPITANT., VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 23.95500 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 47.91000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 47.91000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 23.95500 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 300 REMARK: THE CRYSTAL CONTAINS ONE MONOMER PER ASYMMETRIC UNIT. THE REMARK 300 FUNCTIONAL ENZYME IS A DIMER OF IDENTICAL SUBUNITS. A REMARK 300 CRYSTALLOGRAPHIC 2-FOLD GENERATES TEH BIOLOGICALLY FUNCTIONAL REMARK 300 DIMERIC ENZYME. THE TWO IDENTICAL ACTIVE SITES HAVE BEEN SHOWN TO REMARK 300 ACT INDEPENDENTLY. ONE REACTION PRODUCT MOLECULE (COPROPOPHYRINOGEN- REMARK 300 III) IS IN THE ACTIVE SITE. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 178.46532 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 119.77500 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OE1 GLN A 176 O HOH A 1088 2.08 REMARK 500 NE2 GLN A 274 O HOH A 1305 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 1241 O HOH A 1296 4557 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP A 239 CB - CG - OD2 ANGL. DEV. = 5.9 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 SER A 85 -164.20 -168.03 REMARK 500 ARG A 168 46.40 -93.91 REMARK 500 ASN A 304 32.72 -142.65 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CP3 A 867 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2Q6Z RELATED DB: PDB REMARK 900 G168R APO-ENZYME REMARK 900 RELATED ID: 1RY3 RELATED DB: PDB REMARK 900 WT-UROD IN COMPLEX WITH THE REACTION PRODUCT, COPROPORPHYRINOGEN-III DBREF 2Q71 A 11 366 UNP P06132 DCUP_HUMAN 11 366 SEQADV 2Q71 ARG A 168 UNP P06132 GLY 168 ENGINEERED MUTATION SEQRES 1 A 356 PHE PRO GLU LEU LYS ASN ASP THR PHE LEU ARG ALA ALA SEQRES 2 A 356 TRP GLY GLU GLU THR ASP TYR THR PRO VAL TRP CYS MET SEQRES 3 A 356 ARG GLN ALA GLY ARG TYR LEU PRO GLU PHE ARG GLU THR SEQRES 4 A 356 ARG ALA ALA GLN ASP PHE PHE SER THR CYS ARG SER PRO SEQRES 5 A 356 GLU ALA CYS CYS GLU LEU THR LEU GLN PRO LEU ARG ARG SEQRES 6 A 356 PHE PRO LEU ASP ALA ALA ILE ILE PHE SER ASP ILE LEU SEQRES 7 A 356 VAL VAL PRO GLN ALA LEU GLY MET GLU VAL THR MET VAL SEQRES 8 A 356 PRO GLY LYS GLY PRO SER PHE PRO GLU PRO LEU ARG GLU SEQRES 9 A 356 GLU GLN ASP LEU GLU ARG LEU ARG ASP PRO GLU VAL VAL SEQRES 10 A 356 ALA SER GLU LEU GLY TYR VAL PHE GLN ALA ILE THR LEU SEQRES 11 A 356 THR ARG GLN ARG LEU ALA GLY ARG VAL PRO LEU ILE GLY SEQRES 12 A 356 PHE ALA GLY ALA PRO TRP THR LEU MET THR TYR MET VAL SEQRES 13 A 356 GLU ARG GLY GLY SER SER THR MET ALA GLN ALA LYS ARG SEQRES 14 A 356 TRP LEU TYR GLN ARG PRO GLN ALA SER HIS GLN LEU LEU SEQRES 15 A 356 ARG ILE LEU THR ASP ALA LEU VAL PRO TYR LEU VAL GLY SEQRES 16 A 356 GLN VAL VAL ALA GLY ALA GLN ALA LEU GLN LEU PHE GLU SEQRES 17 A 356 SER HIS ALA GLY HIS LEU GLY PRO GLN LEU PHE ASN LYS SEQRES 18 A 356 PHE ALA LEU PRO TYR ILE ARG ASP VAL ALA LYS GLN VAL SEQRES 19 A 356 LYS ALA ARG LEU ARG GLU ALA GLY LEU ALA PRO VAL PRO SEQRES 20 A 356 MET ILE ILE PHE ALA LYS ASP GLY HIS PHE ALA LEU GLU SEQRES 21 A 356 GLU LEU ALA GLN ALA GLY TYR GLU VAL VAL GLY LEU ASP SEQRES 22 A 356 TRP THR VAL ALA PRO LYS LYS ALA ARG GLU CYS VAL GLY SEQRES 23 A 356 LYS THR VAL THR LEU GLN GLY ASN LEU ASP PRO CYS ALA SEQRES 24 A 356 LEU TYR ALA SER GLU GLU GLU ILE GLY GLN LEU VAL LYS SEQRES 25 A 356 GLN MET LEU ASP ASP PHE GLY PRO HIS ARG TYR ILE ALA SEQRES 26 A 356 ASN LEU GLY HIS GLY LEU TYR PRO ASP MET ASP PRO GLU SEQRES 27 A 356 HIS VAL GLY ALA PHE VAL ASP ALA VAL HIS LYS HIS SER SEQRES 28 A 356 ARG LEU LEU ARG GLN HET CP3 A 867 48 HETNAM CP3 COPROPORPHYRINOGEN III FORMUL 2 CP3 C36 H44 N4 O8 FORMUL 3 HOH *383(H2 O) HELIX 1 1 ASP A 17 GLY A 25 1 9 HELIX 2 2 LEU A 43 ALA A 51 1 9 HELIX 3 3 ASP A 54 ARG A 60 1 7 HELIX 4 4 SER A 61 PHE A 76 1 16 HELIX 5 5 LEU A 88 LEU A 94 1 7 HELIX 6 6 GLU A 114 LEU A 121 5 8 HELIX 7 7 ASP A 123 GLU A 125 5 3 HELIX 8 8 VAL A 126 LEU A 131 1 6 HELIX 9 9 LEU A 131 ALA A 146 1 16 HELIX 10 10 ALA A 157 GLU A 167 1 11 HELIX 11 11 MET A 174 ARG A 184 1 11 HELIX 12 12 ARG A 184 ALA A 209 1 26 HELIX 13 13 HIS A 220 LEU A 224 5 5 HELIX 14 14 GLY A 225 ALA A 233 1 9 HELIX 15 15 ALA A 233 ALA A 251 1 19 HELIX 16 16 GLY A 265 PHE A 267 5 3 HELIX 17 17 ALA A 268 ALA A 273 1 6 HELIX 18 18 ALA A 287 GLY A 296 1 10 HELIX 19 19 ASP A 306 ALA A 312 5 7 HELIX 20 20 SER A 313 GLY A 329 1 17 HELIX 21 21 ASP A 346 LEU A 364 1 19 SHEET 1 A 7 ALA A 81 ILE A 82 0 SHEET 2 A 7 LEU A 151 GLY A 156 1 O ILE A 152 N ALA A 81 SHEET 3 A 7 ALA A 213 GLU A 218 1 O ALA A 213 N GLY A 153 SHEET 4 A 7 MET A 258 ALA A 262 1 O ILE A 259 N LEU A 216 SHEET 5 A 7 VAL A 279 GLY A 281 1 O GLY A 281 N ILE A 260 SHEET 6 A 7 THR A 300 LEU A 305 1 O THR A 300 N VAL A 280 SHEET 7 A 7 TYR A 333 LEU A 337 1 O ILE A 334 N LEU A 301 SHEET 1 B 2 THR A 99 VAL A 101 0 SHEET 2 B 2 GLY A 105 SER A 107 -1 O GLY A 105 N VAL A 101 CISPEP 1 GLY A 303 ASN A 304 0 -3.45 SITE 1 AC1 26 ARG A 37 GLN A 38 ALA A 39 GLY A 40 SITE 2 AC1 26 ARG A 41 PHE A 46 PHE A 55 ILE A 82 SITE 3 AC1 26 ILE A 83 PHE A 84 SER A 85 ASP A 86 SITE 4 AC1 26 ILE A 87 MET A 100 PRO A 106 PHE A 154 SITE 5 AC1 26 TYR A 164 PHE A 217 SER A 219 HIS A 339 SITE 6 AC1 26 HOH A1143 HOH A1306 HOH A1326 HOH A1328 SITE 7 AC1 26 HOH A1350 HOH A1374 CRYST1 103.037 103.037 71.865 90.00 90.00 120.00 P 31 2 1 6 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.009705 0.005603 0.000000 0.00000 SCALE2 0.000000 0.011207 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013915 0.00000